I'd gently scrape and vacuum any existing..........attempt to fill in those gaps between boards. I would make no attempt to fill those gaps. This wood is certainly moving with the seasons.........heater/AC/rain/dry seasons. It's really a part of the "character" of this old floor just like those scabby patches. I'm not mad at you for painting over this for the short term. Whether this is your "forever house" like my current place or you intend to sell the above recommended fixes are very labor intensive and involve substantially more cash out of pocket than----light repairs and paint.
